The invention relates generally to tissue micro array processing and diagnosis of disease.
Tissue micro arrays (TMA) are used for many analytic and diagnostic purposes, one of which is to diagnose diseased tissue at the molecular level. Cancer histopathology diagnosis has been based on cellular morphology using hematoxylin and eosin (H&E) stained biopsy tissue with bright field microscopy. Today, oncogenes are detected with immunohistochemistry (IHC) stains in selected diagnostic exams to prescribe drug therapy with new cancer drugs that are only effective in a fraction of patients. Until now, the process for analyzing TMAs to determine whether a given tissue sample indicates disease and more specifically, a certain type or stage of disease was performed by pathologists looking at a given TMA through a microscope and subjectively rendering a conclusion.
For example, breast cancer is not a single disease but multiple diseases where the tumor phenotype is recognizable at the molecular level; molecular marker quantization is needed for diagnosis to prescribe treatment. β-catenin subcellular distribution in breast cancer has been analyzed using immunohistochemistry (IHC) and immunofluorescence (IF) to predict survival. Treatment of breast cancer by estrogen ablation depends on the tumor having an estrogen receptor. As such, IHC testing for the estrogen receptor (ER) is used to prescribe such hormone ablation therapy. The human epidermal growth factor receptor-2 (Her2) is over expressed in approximately 20-30% of breast cancers associated with an aggressive disease course a poor prognosis. A second IHC stain has been used to test for Her2/neu over-expression. The brown staining is scored visually by a pathologist using categories 0, +1, +2, +3 using bright field microscopy. A short course of the monoclonal antibody trastuzumab (Herceptin®), when administered with docetaxel, is effective in women with breast cancer who have an amplified Her2/neu gene.
Translocation activities are used as indicators of various cancers, including but not limited to breast cancer and other epithelial-based cancers. For example, upon Wnt signaling, unphosphorylated β-catenin accumulates in the cytosol and translocates into the nucleus functioning as a transcription factor for a number of target genes that cause tumor development. In the absence of Wnt signaling in normal tissue, phospho-β-catenin is located at the cell-cell adherens junctions associated with cadherins and is rapidly degraded in the cytosol. Glycogen synthase-3β kinase-3β (GSK3β)-mediated phosphorylation promotes rapid β-catenin degradation in proteasomes. In breast cancer, membranous β-catenin expression correlates with improved survival, while phospho-β-catenin cytosol expression correlates with poor survival. Tamoxifen resistant cell lines undergoing an epithelial to mesenchymal transition involves modulation β-catenin phosphorylation. β-catenin plays a role in other epithelial cancers as well.
Manual analysis of TMAs is expensive and time consuming and necessarily dependent on the pathologist's visual assessment. Although tissue micro-arrays (TMAs) have had the potential to provide a means for high throughput analysis of large patient cohorts, the large amount of information in the TMAs and the high dimensional nature of the data require automated and robust image analysis tools that have not previously been available.